All code, data, and other necessary files needed to reproduce these analyses and figures can be found on my CaribbeanSST GitHub repository. Dropbox links are also provided for large files (netCDF/shape) for download within the Rmarkdown code

Figure 1 | Map of reefs included in SST analyses specific to reef locations. Reef shape files were obtained from the UN Environment World Conservation Monitoring Centre.


Additional exploratory analyses

Historic maximum SST (map)

HadISST (1870 - 2019)

Figure 9 | Maximum SST (\(^\circ\)C) recorded in the entire HadISST dataset (from 1870 to 2019) within each grid (A). The year (B) and month (C) in which each maximum SST was observed is also depicted.


HadISST (1981 - 2019)

Figure 10 | Maximum SST (\(^\circ\)C) recorded in the subset HadISST dataset (1870 - 2019) within each grid (A). The year (B) and month (C) in which each maximum SST was observed is also depicted.


Pathfinder (1981 - 2019)

Figure 11 | Maximum SST (\(^\circ\)C) recorded in the subset Pathfinder dataset (1981 - 2019) within each grid (A).




Historic minimum SST (map)

HadISST (1870 - 2019)

Figure 12 | Minimum SST (\(^\circ\)C) recorded in the entire HadISST dataset (from 1870 to 2019) within each grid (A). The year (B) and month (C) in which each minimum SST was observed is also depicted.


HadISST (1981 - 2019)

Figure 13 | Minimum SST (\(^\circ\)C) recorded in the subset HadISST dataset (1870 - 2019) within each grid (A). The year (B) and month (C) in which each minimum SST was observed is also depicted.


Pathfinder (1981 - 2019)

Figure 14 | Minimum SST (\(^\circ\)C) recorded in the Pathfinder dataset (1870 - 2019) within each grid (A).




Regional SST analyses

Here, I plan to work on binning the reefs into subregions (like in Muñiz-castillo et al 2019) for analyses of SST trends (minimum, maximum, mean, change over time) by these ecoregions.

Another thing to note, I did not crop reefs originally with these shapefiles so I have a few on the western coast of Panama (for example) that technically do not fall within the Caribbean proper. Thoughts on if I should redo all the SST extractions (Figures 2-5) clipping reef locations with these shapefiles?

## OGR data source with driver: ESRI Shapefile 
## Source: "/Users/colleen/Dropbox/Git/CaribbeanSST/data/EcoRegions", layer: "Caribbean_ecoregions"
## with 16 features
## It has 9 fields

Figure 14 | Caribbean ecoregions (A) as established by Spalding et al 2007 included in this analysis and the associate reef locations (B). All marine ecoregion shapefiles and accompanying manuscript can be accessed here. Based on reef selection at the start of the analysis, both the Bermuda and Southern Gulf of Mexico regions have been excluded from the analysis and reefs along the western coast of Central America have been excluded with these shapes.


Figure 15 | Mean SST across coral reefs within each Caribbean Ecoregion at monthly sampling event (HadISST dataset) from 1870 to 2019. Year is represented by colour of each line, changing from blue to red in more recent years.


Figure 16 | Annual mean SST (HadISST) recorded on reefs within each ecoregion (black line - as calculated using the geom_smooth function fit with a general addative model) and 95% confidence interval (grey ribbon). The blue line represents the annual minimum SST across sites within a specific ecoregion and the red line depicts the maximum SST across sites within an ecoregion per year. The grey horizontal dotted line represented the overall mean SST across all reefs within the Caribbean.





Session Information

Last update was 2020-08-23

## R version 3.5.1 (2018-07-02)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS High Sierra 10.13.6
## 
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] grid      stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] repmis_0.5         plotly_4.9.0       gganimate_1.0.6   
##  [4] fields_10.3        maps_3.3.0         spam_2.2-2        
##  [7] dotCall64_1.0-0    binr_1.1           RColorBrewer_1.1-2
## [10] xts_0.12-0         zoo_1.8-6          forcats_0.4.0     
## [13] stringr_1.4.0      dplyr_0.8.3        purrr_0.3.3       
## [16] readr_1.3.1        tidyr_1.0.0        tibble_2.1.3      
## [19] tidyverse_1.3.0    cowplot_1.0.0      ggplot2_3.2.1     
## [22] rgdal_1.4-4        maptools_0.9-5     viridis_0.5.1     
## [25] viridisLite_0.3.0  raster_2.9-23      sp_1.3-1          
## [28] ncdf4_1.16.1       sf_0.7-4          
## 
## loaded via a namespace (and not attached):
##  [1] colorspace_1.4-1      ellipsis_0.3.0        class_7.3-15         
##  [4] fs_1.3.1              rstudioapi_0.10       farver_2.0.1         
##  [7] fansi_0.4.1           lubridate_1.7.4       xml2_1.2.2           
## [10] splines_3.5.1         codetools_0.2-16      R.methodsS3_1.8.0    
## [13] knitr_1.25            zeallot_0.1.0         jsonlite_1.6         
## [16] Cairo_1.5-10          broom_0.5.2           dbplyr_1.4.2         
## [19] R.oo_1.23.0           rgeos_0.4-3           shiny_1.4.0          
## [22] compiler_3.5.1        httr_1.4.1            backports_1.1.5      
## [25] Matrix_1.2-17         assertthat_0.2.1      fastmap_1.0.1        
## [28] lazyeval_0.2.2        cli_2.0.1             later_1.0.0          
## [31] tweenr_1.0.1          htmltools_0.4.0       prettyunits_1.0.2    
## [34] tools_3.5.1           gtable_0.3.0          glue_1.3.1           
## [37] Rcpp_1.0.3            cellranger_1.1.0      vctrs_0.2.1          
## [40] nlme_3.1-140          transformr_0.1.2.9000 crosstalk_1.0.0      
## [43] xfun_0.8              rvest_0.3.5           mime_0.7             
## [46] lpSolve_5.6.15        lifecycle_0.1.0       scales_1.1.0         
## [49] hms_0.5.3             promises_1.1.0        yaml_2.2.0           
## [52] gridExtra_2.3         stringi_1.4.5         e1071_1.7-2          
## [55] rlang_0.4.2           pkgconfig_2.0.3       evaluate_0.14        
## [58] lattice_0.20-41       htmlwidgets_1.3       labeling_0.3         
## [61] tidyselect_0.2.5      plyr_1.8.5            magrittr_1.5         
## [64] R6_2.4.1              magick_2.2            generics_0.0.2       
## [67] DBI_1.0.0             mgcv_1.8-28           pillar_1.4.3         
## [70] haven_2.2.0           foreign_0.8-71        withr_2.1.2          
## [73] units_0.6-3           modelr_0.1.5          crayon_1.3.4         
## [76] KernSmooth_2.23-15    rmarkdown_1.16        progress_1.2.2       
## [79] readxl_1.3.1          data.table_1.12.2     reprex_0.3.0         
## [82] digest_0.6.23         classInt_0.3-3        xtable_1.8-4         
## [85] R.cache_0.14.0        httpuv_1.5.2          R.utils_2.9.2        
## [88] munsell_0.5.0